Molecular Biology Data Sources: Structure

• RCSB Protein Data Bank (PDB)
• Cambridge Structural Database (CSD)

Access RCSB PDB

What is it?

• Worldwide repository for information about 3D structures of biological macromolecules e.g. ribosomes
• Provides tools for structure visualization
• Research Collaboratory for Structural Bioinformatics (RCSB) manages RCSB PDB
  • Staff located at Rutgers University and University of California, San Diego
  • A deposition, processing and distribution center for Worldwide Protein Data Bank (wwPDB)
• RCSB PDB built using PDB archive, which is maintained by wwPDB
  • Archive updated weekly

Access

• Public access
• Data files in RCSB PDB archive are free of all copyright restrictions
• Molecule of the Month illustrations and articles are copyrighted
• All other articles and text on the site are copyrighted
• For further information on use of RCSB PDB materials, visit RCSB PDB Policies & References

How to Retrieve Data

• Searching
  • Where to start
    • To search for structures, enter keyword or PDB ID into search box at the top of homepage
    •  Click on Author button above search box to search by author name
  • Multiple search and browse options available, for more information, visit Searching the RCSB PDB
•  Multiple options available for download of data files, including maintaining a local copy of all PDB files
  • For more information, select options from the Tool box in the right menu on the RCSB PDB homepage

Submissions

• Accepts all experimentally determined structures that meet minimum requirements
  • Three dimensional coordinates
  • Information about composition of structure
  • Information about experiment performed
  • Details of structure determination steps
  • Author contact information
• Types of structures accepted:
  • Polypeptides and their complexes
    • All gene products
    • All naturally-occurring peptides that are non-ribosomal in origin
    • All peptidic repeat units of larger polymers
    • Synthetic peptides with at least 24 residues in a polymer chain
  • Polynucleotides of 4 or more residues, and their complexes
  • Polysaccharides of 4 or more residues, and their complexes
•  RCSB PDB has several tools for the validation and deposition of data, visit RCSB PDB Data Validation & Deposition Services for more information
•  Length of time structure held from public release selected during deposition

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Access CSD

What is it?

• Repository of small-molecule organic and metal-organic crystal structures compiled by the Cambridge Crystallographic Data Centre (CCDC), a company that started at the University of Cambridge
• Data from:
  • Publications
  • Private communications via direct deposit
• Does not store:
  • Polypeptides and polysaccharides
  • Oligonucleotides
  • Inorganic structures
  • Metals and alloys
• Part of the CSD System, which includes software for:
  • Search and information retrieval
  • Structure visualization
  • Statistical analysis of retrieved data
  • Knowledge bases derived from CSD

Access

• Anyone can request data for bona fide research purposes
• CSD System must be purchased
  • UNC Research Computing has licenses running on Killdevil
  • For further instructions on accessing CSD via Killdevil, please visit UNC Help & Support: Cambridge Structural Database

How to Retrieve Data

• May request data after associated paper has been published
  • Use online Request Form
  • One paper per request
  • Need full journal citation and CCDC Deposition Number, which should be in paper
  • Data sent in CIF format free of charge
• Currently only data published after 1994 is available via request
• Data published before 1994 is available through CSD distributed with CSD System (see above for access instructions)

Submissions

• Accepts crystal structure data from X-ray, neutron diffraction and powder studies using a constrained refinement for:
  • Organic compounds
  • Metal-organic compounds
  • Metal carbonyls
  • Boron compounds containing one or more B-H or B-OH bond and borazines
    
  • Ring compounds containing any two of the following elements: N, P, S, Se and Te
• Types of depositions:
  • Pre-publication
  • Published
  • Private communication: structure not intended for publication
• For further information, visit Deposit a Structure

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